Tag Archives: hapmap

十一 15

hapmap计划资源收集

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官网是：http://hapmap.ncbi.nlm.nih.gov/index.html.en

所有的数据都放在ncbi上面：ftp://ftp.ncbi.nlm.nih.gov/hapmap/
现在一般用这个计划的数据主要是拿自己得到的突变数据来跟这个hapmap计划的人种突变数据对比。
有芯片数据，也有WES和WGS数据，随着时间的推进，平台也在更新：
Jul 07 2009 00:00    Directory affy100k
Mar 05 2010 00:00    Directory affy500k
Jun 02 2010 00:00    Directory hapmap3_affy6.0
当然，数据也在更新
Jul 07 2009 00:00    Directory 2005-03_phaseI
Dec 03 2009 00:00    Directory 2005-11_phaseII
Jul 07 2009 00:00    Directory 2007-03
Jul 07 2009 00:00    Directory 2008-03
Jul 07 2009 00:00    Directory 2008-07_phaseIII
Jul 07 2009 00:00    Directory 2008-10_phaseII
Jul 07 2009 00:00    Directory 2009-01_phaseIII
Jul 07 2009 00:00    Directory 2009-02_phaseII+III
Aug 18 2010 00:00    Directory 2010-05_phaseIII
Sep 19 2010 00:00    Directory 2010-08_phaseII+III
数据都被整合好了：
  • Bulk data
    • Genotypes: Individual genotype data submitted to the DCC to date. Phase 3 data is available in PLINK format and HapMap format.
    • Frequencies: Allele & genotype frequencies compiled from genotyping data submitted to the DCC to date. These have also been submitted to dbSNP and should be available in the next dbSNP build.
    • LD Data: Linkage disequilibrium properties D', LOD , R2 compiled from the genotype data to date
    • Phasing Data: Phasing data generated using the PHASE software, compiled from the genotype data to date.
    • Allocated SNPs: dbSNP reference SNP clusters that have been picked and prioritized for genotyping according to several criteria (see info on how SNPs were selected). The file 00README contains per-chromosome SNP counts and further details.
    • CNV Genotypes: CNV data from HapMap3 samples.
    • Recombination rates and Hotspots: Recombination rates and hotspots compiled from the genotyping data.
    • SNP assays: Details about assays submitted to the DCC to date. PCR primers, extension probes etc., specific to each genotyping platform.
    • Perlegen amplicons: Details for mapping Perlegen amplicons to HapMap assayLSID. For primer sequences, see Perlegen's Long Range PCR Amplicon data.
    • Raw data: Raw signal intensity data from HapMap genotypes. Currently includes data from Affymetrix GeneChip 100k and 500k Mapping Arrays.
    • Inferred genotypes: Genotypes inferred using the method of Burdick et al. Nat Genet 38:1002-4.
    • Mitochondrial and chrY haplogroups: Classification of phase I HapMap samples into mtDNA and chrY haplogroups. The distribution shown in Table 4 of the HapMap phase I paper (Nat Genet 38:1002-4) corresponds to unrelated parents in each one of the populations analyzed.
同时也发了很多篇文章：
  • The International HapMap Consortium. Integrating common and rare genetic variation in diverse human populations.
    Nature 467, 52-58. 2010. [Abstract] [PDF] [Supplementary information]
  • The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs.
    Nature 449, 851-861. 2007. [Abstract] [PDF] [Supplementary information]
  • The International HapMap Consortium. A Haplotype Map of the Human Genome. 
    Nature 437, 1299-1320. 2005. [Abstract] [PDF] [Supplementary information]
  • The International HapMap Consortium. The International HapMap Project.
    Nature 426, 789-796. 2003. [Abstract] [PDF] [Supplementary information]
  • The International HapMap Consortium. Integrating Ethics and Science in the International HapMap Project. 
    Nature Reviews Genetics 5, 467 -475. 2004. [Abstract] [PDF]
  • Thorisson, G.A., Smith, A.V., Krishnan, L., and Stein, L.D. The International HapMap Project Web site.
    Genome Research,15:1591-1593. 2005. [Abstract] [PDF]